Shading created by intercropping reduces the photosynthetic capacity of soybean plants but also directly affects the pod setting process of soybean. However, which of the changed aspects induce the yield differences in intercropped soybean cultivars is still unknown. Four soybean cultivars with similar yield and growth and development processes in monoculture were selected by a pre-experiment. Field experiments were carried out from 2015 to 2017 to investigate the leaf photosynthetic parameters, total biomass, reproductive characteristics, yield and yield components of soybean. The yield of soybean cultivars was significantly decreased in intercropping systems and the yield of cultivars (cvs.) ZH39 and QH34 were considerably higher than those of cvs. HD19 and HD20. Besides, the pod and seed number and harvest index were also reduced by intercropping and the yield components of cvs. ZH39 and QH34 in intercropping were significantly higher than those of cvs. HD19 and HD20, other than the seed size. Although the parameters of leaf photosynthetic capacity (leaf area index, net photosynthetic rate, and chlorophyll content) of soybean were changed by intercropping, there was no significant difference among cultivars. Additionally, the CGRR1–R5
(crop growth rate between R1 and R5) of intercropped soybean was lower than that of monoculture, while no significant differences were observed in different cultivars. The reproductive biomass at R5 was significantly different among soybean cultivars, and the reproductive partitioning and seed set efficiency of different cultivars were varied by the reproductive biomass at R5. Therefore, high-yielding cultivars in intercropping can achieve higher yield due to more reproductive structures survived at R5.
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